Educational transformation in the 21st century demands in-depth knowledge and understanding in order to promote the development of higher-order thinking skills (HOTS). However, the most commonly reported problem with respect to developing a knowledge of chemistry is poor mastery of basic concepts. Chemistry laboratory educational activities are shown to be less effective in developing an optimum conceptual understanding and HOTS among students. One factor is a lack of effective assessment and evaluation tools. Therefore, the primary focus of this study is to explore concept maps as an assessment tool in order to move students' thinking skills to a higher level during laboratory learning activities. An embedded mixed method design is used in this study, which has also employed a pre-experimental research design. This design triangulates quantitative and qualitative data, which are combined to strengthen the findings. A low-directed concept mapping technique, convergence scoring method, and pre-post laboratory concept map were used in this study. An electrolysis HOTS test was used as the research instrument in order to measure the level of student achievement with respect to high-level questions. In addition, the thought process that is involved when students construct concept maps has been explored and studied in detail by utilising a think-aloud protocol. Results showed a positive development towards understanding and higher level thinking skills in students with respect to electrolysis concepts learned through chemistry laboratory activities. An investigation of the students' thinking processes showed that high-achieving students were more capable of giving a content-based explanation of electrolysis and engaged in monitoring activities more often while building a concept map. Nonetheless, all categories of students managed to show a positive increase in the activities of explanation and monitoring during the construction of concept maps after they were exposed to the assessment tool in the laboratory learning activities. In conclusion, the assessment activity using concept maps in laboratory learning activities has a positive impact on students' understanding and stimulates students to increase their HOTS.